Saccharomyces cerevisiae Reference Assembly Panel Database (ScRAPdb)
Saccharomyces cerevisiae Reference Assembly Panel Database (ScRAPdb)
A searchable table of the S. cerevisiae pangenome ORFs defined in Peter et al. (2018) Nature (LINK) is provided below. The listed core/accessory classification and origin assignment are based on the original study. Click on the PanORF ID to find out the detailed presence/absence pattern of the corresponding pangenome ORF in both ScRAPdb and the 1002ScGP strain collections (which were recalculated by ScRAPdb).
| PanORF ID | SGD systematic Name | SGD standard name | Alias | Description | Type | Origin assignment | Mostly likely origin species | NCBI megablast hit |
|---|---|---|---|---|---|---|---|---|
| 1988-YBR007C | YBR007C | DSF2 | NA | Deletion suppressor of mpt5 mutation; relocalizes from bud neck to cytoplasm upon DNA replication stress | Accessory | Ancestral | NA | NA |
| 1989-YBR008C | YBR008C | FLR1 | NA | Plasma membrane transporter of the major facilitator superfamily; member of the 12-spanner drug:H(+) antiporter DHA1 family; involved in efflux of fluconazole, diazaborine, benomyl, methotrexate, and other drugs; expression induced in cells treated with the mycotoxin patulin; relocalizes from nucleus to plasma membrane upon DNA replication stress | Accessory | Ancestral | NA | NA |
| 1990-YBR009C_NumOfGenes_2 | YBR009C | HHF1 | histone H4 | Histone H4; core histone protein required for chromatin assembly and chromosome function; one of two identical histone proteins (see also HHF2); contributes to telomeric silencing; N-terminal domain involved in maintaining genomic integrity | Core | NA | NA | NA |
| 1991-YBR010W | YBR010W | HHT1 | histone H3|SIN2|BUR5 | Histone H3; core histone protein required for chromatin assembly, part of heterochromatin-mediated telomeric and HM silencing; one of two identical histone H3 proteins (see HHT2); regulated by acetylation, methylation, and phosphorylation; H3K14 acetylation plays an important role in the unfolding of strongly positioned nucleosomes during repair of UV damage | Accessory | Ancestral | NA | NA |
| 1992-YBR011C | YBR011C | IPP1 | inorganic diphosphatase IPP1|PPA1 | Cytoplasmic inorganic pyrophosphatase (PPase); homodimer that catalyzes the rapid exchange of oxygens from Pi with water, highly expressed and essential for viability, active-site residues show identity to those from E. coli PPase | Core | NA | NA | NA |
| 1993-YBR012C | YBR012C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; expression induced by iron-regulated transcriptional activator Aft2p | Accessory | Introgression | S. paradoxus | NA |
| 1994-YBR013C | YBR013C | NA | NA | Putative protein of unknown function; haploid deletion mutant exhibits synthetic phenotype with alpha-synuclein; SWAT-GFP fusion protein localizes to the endoplasmic reticulum while mCherry fusion protein localizes to both the endoplasmic reticulum and vacuole | Accessory | Ancestral | NA | NA |
| 1995-YBR014C | YBR014C | GRX7 | glutathione-disulfide reductase GRX7 | Cis-golgi localized monothiol glutaredoxin; more similar in activity to dithiol than other monothiol glutaredoxins; involved in the oxidative stress response; does not bind metal ions; GRX7 has a paralog, GRX6, that arose from the whole genome duplication | Core | NA | NA | NA |
| 1996-YBR015C | YBR015C | MNN2 | alpha-1,2-mannosyltransferase MNN2|LDB8|CRV4|TTP1 | Alpha-1,2-mannosyltransferase; responsible for addition of the first alpha-1,2-linked mannose to form the branches on the mannan backbone of oligosaccharides, localizes to an early Golgi compartment | Core | NA | NA | NA |
| 1997-YBR016W | YBR016W | NA | NA | Tail-anchored plasma membrane protein with a conserved CYSTM module; predicted to be palmitoylated; has similarity to hydrophilins, which are involved in the adaptive response to hyperosmotic conditions; YBR016W has a paralog, YDL012C, that arose from the whole genome duplication | Core | NA | NA | NA |
| 1998-YBR017C | YBR017C | KAP104 | NA | Transportin or cytosolic karyopherin beta 2; functions in the rg-nuclear localization signal-mediated nuclear import/reimport of mRNA-binding proteins Nab2p and Hrp1p; regulates asymmetric protein synthesis in daughter cells during mitosis | Accessory | Ancestral | NA | NA |
| 1999-YBR018C | YBR018C | GAL7 | UDP-glucose:hexose-1-phosphate uridylyltransferase | Galactose-1-phosphate uridyl transferase; synthesizes glucose-1-phosphate and UDP-galactose from UDP-D-glucose and alpha-D-galactose-1-phosphate in the second step of galactose catabolism; human homolog UGP2 can complement yeast null mutant | Accessory | Ancestral | NA | NA |
| 2000-YBR019C | YBR019C | GAL10 | bifunctional UDP-glucose 4-epimerase/aldose 1-epimerase | UDP-glucose-4-epimerase; catalyzes interconversion of UDP-galactose and UDP-D-glucose in galactose metabolism; also catalyzes conversion of alpha-D-glucose or alpha-D-galactose to their beta-anomers; human homolog GALE implicated in galactosemia, can complement yeast null mutant | Accessory | Ancestral | NA | NA |
| 2001-YBR020W | YBR020W | GAL1 | galactokinase | Galactokinase; phosphorylates alpha-D-galactose to alpha-D-galactose-1-phosphate in the first step of galactose catabolism; expression regulated by Gal4p; human homolog GALK2 complements yeast null mutant; GAL1 has a paralog, GAL3, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 2002-YBR021W | YBR021W | FUR4 | uracil permease | Plasma membrane localized uracil permease; expression is tightly regulated by uracil levels and environmental cues; conformational alterations induced by unfolding or substrate binding result in Rsp5p-mediated ubiquitination and degradation | Core | NA | NA | NA |